Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate BWI76_RS08460 BWI76_RS08460 dicarboxylate/amino acid:cation symporter
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__Koxy:BWI76_RS08460 Length = 435 Score = 286 bits (732), Expect = 8e-82 Identities = 159/415 (38%), Positives = 248/415 (59%), Gaps = 13/415 (3%) Query: 1 MRKIGLAWQIFIGLILGIIVGAIFYGNPKV---AAYLQPIG---DIFLRLIKMIVIPIVI 54 M+KI L I +GLILG+I G I +Y Q I IFLR++KMI+ P+VI Sbjct: 1 MKKISLTKMIILGLILGMIAGVIINNMASADTAKSYAQDISIFTTIFLRMVKMIIAPLVI 60 Query: 55 SSLVVGVASVGDLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTD 114 S+LVVG+A +GD K LG++ KT F + ++I +GL+ N+FQPGAG+N + Sbjct: 61 STLVVGIAKMGDAKTLGRIFSKTFFLFICASLLSIALGLVIVNLFQPGAGINFVPHDAGA 120 Query: 115 IQSYVDTTNEVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKP 174 + + + + ++ + VP +I ++++ ++L I+ FS+ G +AAIGEK +P Sbjct: 121 VAAV-----QSEPFTLKVFISHAVPTSIVDAMARNEILQIVVFSIFLGCSLAAIGEKAEP 175 Query: 175 VLQFFQGTAEAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFF 234 +++ M +T +M FAP VFA I +++ G+ ++ + Y T L Sbjct: 176 IVKVLDSLVHVMLKLTGYVMLFAPLTVFAAISGLIAERGLGVMVSAGIFMGEFYLT-LGM 234 Query: 235 IFAVLGGVAKLF-GINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSF 293 ++A+L G++ + G I + K + + +LA++T+SSE P +DK+EKFG I SF Sbjct: 235 LWAILIGLSTVIVGPCISRLTKAIFEPALLAFTTSSSEAAFPGTLDKLEKFGVSSKIASF 294 Query: 294 VIPTGYSFNLDGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFV 353 V+P GYSFNL GS Y + A +FIAQ + +S+ +QI++LL+LM+TSKG+AGVP S V Sbjct: 295 VLPIGYSFNLVGSMAYCSFATVFIAQACNVHLSMGEQITMLLILMLTSKGMAGVPRASMV 354 Query: 354 VLLATLGTVGIPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEE 408 V+ ATL IP GL + G+D LDM R+A NV+ N++ A I+ +WEG++ E Sbjct: 355 VIAATLNQFNIPEAGLILLMGVDPFLDMGRSATNVMSNAMGAAIVGRWEGEHYGE 409 Lambda K H 0.326 0.143 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 412 Number of extensions: 21 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 421 Length of database: 435 Length adjustment: 32 Effective length of query: 389 Effective length of database: 403 Effective search space: 156767 Effective search space used: 156767 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory